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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: Oct 23, 2025

Preparation of Cytoplasmic and Nuclear Long RNAs from Primary and Cultured Cells

Preparation of Cytoplasmic and Nuclear Long RNAs from Primary and Cultured Cells

Published on: April 7, 2023

Nuclear RNA Isolation and Sequencing.

Navroop K Dhaliwal¹, Jennifer A Mitchell²

¹Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.

Methods in Molecular Biology (Clifton, N.J.)

|August 21, 2021

Summary

This summary is machine-generated.

Nuclear RNA sequencing (nucRNA-seq) captures unspliced and spliced transcripts, including long non-coding RNAs, offering a more complete view of gene expression than poly (A) RNA sequencing.

Keywords:

Cellular fractionation LncRNA Massively parallel sequencing Nuclear RNA Transcriptome profiling

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Last Updated: Oct 23, 2025

Preparation of Cytoplasmic and Nuclear Long RNAs from Primary and Cultured Cells

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Published on: April 7, 2023

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Nuclei Isolation from Whole Tissue using a Detergent and Enzyme-Free Method

Nuclei Isolation from Whole Tissue using a Detergent and Enzyme-Free Method

Published on: June 24, 2020

Area of Science:

Molecular Biology
Genomics
Transcriptomics

Background:

Traditional transcriptome studies focus on polyadenylated (poly (A)) RNA, providing steady-state mRNA levels.
Poly (A) RNA sequencing may not accurately reflect transcriptional regulation or capture non-polyadenylated transcripts like enhancer RNAs (eRNAs).

Purpose of the Study:

To introduce and validate nuclear RNA sequencing (nucRNA-seq) as a method to comprehensively analyze the transcriptome.
To overcome limitations of poly (A) RNA sequencing in capturing full transcriptional output.

Main Methods:

Nuclear RNA was isolated from cells.
Isolated nuclear RNAs were sequenced and quantified.
The method captures both spliced and unspliced transcripts, including long non-coding RNAs.

Main Results:

nucRNA-seq provides a more comprehensive view of the transcriptional landscape compared to poly (A) RNA sequencing.
The method successfully identifies nuclear-retained long non-coding RNAs and unspliced transcripts.
nucRNA-seq offers insights into transcriptional regulation not discernible from steady-state mRNA levels.

Conclusions:

Nuclear RNA sequencing (nucRNA-seq) is a valuable tool for studying the full spectrum of RNA transcription.
This method enhances our understanding of gene expression regulation, particularly for non-coding RNAs and nascent transcripts.